scholarly journals PAirwise Sequence Comparison (PASC) and Its Application in the Classification of Filoviruses

Viruses ◽  
2012 ◽  
Vol 4 (8) ◽  
pp. 1318-1327 ◽  
Author(s):  
Yiming Bao ◽  
Vyacheslav Chetvernin ◽  
Tatiana Tatusova
Keyword(s):  
Sequence Comparison ◽  
Pairwise Sequence Comparison

scholarly journals Understanding the Genetic Diversity of Picobirnavirus: A Classification Update Based on Phylogenetic and Pairwise Sequence Comparison Approaches

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1476
Author(s):  
Lester J. Perez ◽  
Gavin A. Cloherty ◽  
Michael G. Berg
Keyword(s):  
Genetic Diversity ◽  
Sequence Comparison ◽  
Complete Resolution ◽  
Pairwise Distance ◽  
Pairwise Sequence Comparison ◽  
Double Stranded Rna ◽  
Phylogenetic Marker ◽  
High Degree ◽  
Phylogenetic Noise

Picobirnaviruses (PBVs) are small, double stranded RNA viruses with an ability to infect a myriad of hosts and possessing a high degree of genetic diversity. PBVs are currently classified into two genogroups based upon classification of a 200 nt sequence of RdRp. We demonstrate here that this phylogenetic marker is saturated, affected by homoplasy, and has high phylogenetic noise, resulting in 34% unsolved topologies. By contrast, full-length RdRp sequences provide reliable topologies that allow ancestralism of members to be correctly inferred. MAFFT alignment and maximum likelihood trees were established as the optimal methods to determine phylogenetic relationships, providing complete resolution of PBV RdRp and capsid taxa, each into three monophyletic groupings. Pairwise distance calculations revealed these lineages represent three species. For RdRp, the application of cutoffs determined by theoretical taxonomic distributions indicates that there are five genotypes in species 1, eight genotypes in species 2, and three genotypes in species 3. Capsids were also divided into three species, but sequences did not segregate into statistically supported subdivisions, indicating that diversity is lower than RdRp. We thus propose the adoption of a new nomenclature to indicate the species of each segment (e.g., PBV-C1R2).

scholarly journals Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
He-Teng Zhang ◽  
Hao Wang ◽  
Hai-Sheng Wu ◽  
Jian Zeng ◽  
Yan Yang
Keyword(s):  
Human Papillomavirus ◽  
Bacterial Community ◽  
Pregnant Women ◽  
Sequence Comparison ◽  
Pairwise Sequence Comparison ◽  
Vaginal Secretion ◽  
The Family ◽  
Complete Genomes ◽  
Different Types ◽  
Vaginal Tract

Abstract Background Although some studies have investigated the bacterial community in vaginal tract of pregnant women, there are few reports about the viral community (virome) in this type of microenvironment. Methods To investigate the composition of virome in vaginal secretion samples, 40 vaginal secretion samples from pregnant women with vaginitis and 20 vaginal secretion samples from pregnant women without vaginitis, pooled into 4 and 2 sample pools, respectively, were subjected to viral metagenomic analysis. Results Results indicated virus sequences showing similarity to human papillomavirus (HPV), anellovirus, and norovirus were recovered from this cohort of pregnant women. Further analysis indicated that 15 different defined types and one unclassified type of HPV were detected from pregnant women with vaginitis while only 3 defined types of HPV were detected in pregnant women without vaginitis. Five different groups of viruses from the family Anelloviridae were present in pregnant women with but none of them were detected in pregnant women without vaginitis. Norovirus was detected in 3 out of the 4 sample pools from pregnant women with vaginitis but none in the pregnant women without vaginitis. Twelve complete genomes belonging to 10 different types of HPV, and 5 novel anllovirus genomes belonging 2 different genera in Anelloviridae were acquired from these libraries, based on which phylogenetical analysis and pairwise sequence comparison were performed. Phageome in these samples was also briefly characterized and compared between two groups. Conclusion Our data suggested that virome might play an important role in the progression of vaginitis in pregnant women.

Sequence comparison and classification of beet luteovirus isolates

1995 ◽  
Vol 140 (12) ◽  
pp. 2183-2200 ◽  
Author(s):  
J. R. de Miranda ◽  
M. Stevens ◽  
E. de Bruyne ◽  
H. G. Smith ◽  
C. Bird ◽  
...  
Keyword(s):  
Sequence Comparison

Dot Matrix Pairwise Sequence Comparison

2007 ◽  
Vol 2007 (24) ◽  
pp. pdb.top31-pdb.top31 ◽  
Author(s):  
D. W. Mount
Keyword(s):  
Sequence Comparison ◽  
Pairwise Sequence Comparison

scholarly journals A sequential development towards a unified approach to protein sequence comparison based on classified groups of amino acids

2018 ◽  
Vol 7 (2) ◽  
pp. 678
Author(s):  
Soumen Ghosh ◽  
Jayanta Pal ◽  
Bansibadan Maji ◽  
Dilip Kumar Bhattacharya
Keyword(s):  
Amino Acids ◽  
Protein Sequence ◽  
Sequence Comparison ◽  
Protein Sequences ◽  
Group Classification ◽  
Unified Approach ◽  
The Unified Method ◽  
Protein Sequence Comparison ◽  
Unified Method

The methods of comparison of protein sequences based on different classified groups of amino acids add a significant contribution to the literature of protein sequence comparison. But the methods vary with choice of different classified groups. Therefore, the purpose of the paper is to develop a unified approach towards the analysis of protein sequence comparison based on classification of amino acids in different groups of different cardinality. The paper considers 4 group classification, 5 group classification and 6 group classifications of amino acids, and in each case it applies the unified method for comparing two types of protein sequences, viz., 9 proteins of ND5 category and 50 Corona virus Spike Proteins. The results agree with those, which were obtained earlier by other methods based on classified groups of amino acids. An-yway it is found that the present unified formula is relatively simpler and fundamentally different from the earlier ones. Further, it can be applied conveniently in comparison of protein sequences based on all different types of classified groups of amino acids.

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